SYSTEMATICS

• Phylogeny


  The study of the evolutionary history and relationships among individuals or group of organisms

  
• Phylogenetic tree


  • A diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor
  • Attempt to reconstruct evolutionary ancestors
  • Estimate time of divergence from ancestor

  
• Phylogenetic analysis have become central to understanding biodiversity, evolution and genomes

  
• Relationships in phylogenetic tree

  Captured by the topology (branching order) and amount of evolutionary change (branch lengths) between nodes

  
• The role of the root is to add direction to these relationships and clearly define ancestry
• Applications of phylogenetic trees


  • Classification of organisms
  • Forensics (e.g. HIV virus mutation)
  • Predicting evolution of influenza viruses
  • Predicting functions of uncharacterized genes (orthologue detection)
  • Drug discovery
  • Bioinformatics
  • Vaccine development
• The term 'phylogeny' introduced by Ernst Haeckel


  1866
• Ernst Haeckel's recapitulation theory was widely accepted during late 19th century but has been rejected in the modern world
• Darwin's 'On The Origin of Species' convinced many biologists to accept common ancestry and start building phylogenies
• Phylogenetic tree


  A two dimensional graph showing evolutionary relationships between organisms or genes from various organisms

  
• Phylogenetic trees are a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships

  
• Types of phylogenetic trees

  • Rooted trees
  • Unrooted trees

  
• Rooted tree


  • Has a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram
  • The three domains (Bacteria, Archaea, and Eukarya) diverge from a single point and branch off

  
• Bifurcating tree


  • Has a maximum of 2 descendants arising from each of the interior nodes
• Multi-furcating tree


  • Has multiple descendants arising from each of the interior nodes
• Unrooted tree

  • Doesn't show a common ancestor but does show relationships among taxa

  
• Taxon


  A formally named group represented by the leaves of a phylogenetic tree

  
• Branch


  Represents the persistence of a lineage through time, may subtend one or many leaves
• Node


  Represents the last common ancestors of organisms at the tips of the descendant lineages
• External branch


  Connects a tip to a node
• Internal branch


  Connects two nodes
• Cladogenesis


  Branching on an evolutionary tree, where an ancestral lineage splits to give rise to two or more descendant lineages

  
• Clade


  A grouping on a tree that includes a node and all of the lineages descended from that node
• Monophyletic clade

  A taxon that includes all descendants of an inferred ancestor, characterized by one or more apomorphies (derived character states)
• Paraphyletic clade


  An assemblage that is constructed by taking a clade and removing one or more smaller clades, characterized by one or more plesiomorphies (character states inherited from ancestors but not present in all of their descendants)
• Polyphyletic clade


  An assemblage that is neither monophyletic nor paraphyletic, characterized by one or more homoplasies (character states which have converged or reverted so as to be the same but which have not been inherited from a common ancestor)
• Phylogenetic inference is the practice of reconstructing the evolutionary history of related species by grouping them in successively more inclusive sets based on shared ancestry

  
• Methods for constructing phylogenetic trees

  • Character-based methods
  • Distance methods
• Character-based methods


  Use the aligned characters, such as DNA or protein sequences, directly during tree inference
• Maximum parsimony


  An optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is selected
• Maximum likelihood


  A method that represents an additional opportunity to evaluate trees with variations in mutation rates in different lineages, and can be used to explore relationships among more diverse sequences and conditions not well handled by maximum parsimony methods
• Maximum Likelihood


  An additional opportunity to evaluate trees with variations in mutation rates in different lineage
• Maximum Likelihood (ML) in phylogeny


  • A method used to figure out the most likely evolutionary tree (phylogeny) based on genetic data
  • It tries to find the tree that makes the sequences the most probable by calculating the likelihood of the data given a particular tree and then finds the tree that maximizes this likelihood
• Distance-based method


  Constructs phylogenetic trees based on the amount of distance or dissimilarity between aligned sequences, transforms sequence data into pairwise distances and then uses the matrix for tree building
• Algorithms used in distance method

  • UPGMA (Unweighted Pair Group Method using Arithmetic Average)
  • Neighbour joining method
• UPGMA


  Simplest algorithm for tree construction, groups species together based on their similarity in genetic data and builds the tree in a way that reflects these similarities, assumes constant rates of evolution across lineages

  
• Steps in UPGMA


  1. Calculate pairwise distances

  2. Group species into clusters based on similarities

  3. Calculate average distance for each cluster

  4. Join clusters with smallest average distance

  5. Repeat until complete tree is built
• Neighbor-Joining (NJ) method


  Iteratively builds the tree by joining pairs of species that are most closely related based on their genetic distances, aims to find the tree structure that best reflects the evolutionary relationships between species
• Phylogenetic tree reconstruction


  1. Sequence alignment

  2. Determining substitution model

  3. Tree building

  4. Tree evaluation